The determination of melt distribution in the crust and the nature of the crust–mantle boundary (the ‘Moho’) is fundamental to the understanding of crustal accretion processes at oceanic spreading centres. Upper-crustal magma chambers have been imaged beneath fast- and intermediate-spreading centres but it has been difficult to image structures beneath these magma sills. Using three-dimensional seismic reflection images, here we report the presence of Moho reflections beneath a crustal magma chamber at the 9° 03′ N overlapping spreading centre, East Pacific Rise. Our observations highlight the formation of the Moho at zero-aged crust. Over a distance of less than 7 km along the ridge crest, a rapid increase in two-way travel time of seismic waves between the magma chamber and Moho reflections is observed, which we suggest is due to a melt anomaly in the lower crust. The amplitude versus offset variation of reflections from the magma chamber shows a coincident region of higher melt fraction overlying this anomalous region, supporting the conclusion of additional melt at depth.